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Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.

Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S - BMC Bioinformatics (2009)

Bottom Line: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation.GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering.GOmir can freely be downloaded BRFAA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cell & Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece. mroubelaki@bioacademy.gr

ABSTRACT

Background: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation. Predicting or verifying mRNA targets of specific miRNAs is a difficult process of great importance.

Results: GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application.

Conclusion: GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering. Additionally, a reverse search initiated by a potential target can also be conducted. GOmir can freely be downloaded BRFAA.

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JTarget main menu. (A) Jtarget interface (B) The target genes of miR-21 as listed by the procedure "Compare All'' (4 databases).
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Figure 1: JTarget main menu. (A) Jtarget interface (B) The target genes of miR-21 as listed by the procedure "Compare All'' (4 databases).

Mentions: JTarget main goal is to find the target genes of a given miRNA derived from 1 to 6 databases and compare any possible combination of the results from these databases. The available databases are TargetScan, miRanda, RNAhybrid, PicTar-4 way, PicTar-5 way and TarBase. Following the insertion of a specific miRNA name, 3 possible scenarios are given. The user can obtain the resulting target genes from: a) one database only, b) two or more databases or c) all combined databases. JTarget contains text fields, buttons and one central text area for the interaction with the user (Figure 1A). To find the target genes of a miRNA from a single database, the "Search by miRNA" option has to be selected and a miRNA name (e.g. miR-21) should be given. Then, a database (e.g. TargetScan) should be marked and the results are presented in the central text area by clicking the "Find Targets" button. The common results from 2 or more databases can be obtained by marking the desirable databases and clicking the "Compare database results" button. The available databases are: TargetScan, miRanda, RNAhybrid, PicTar-4 way, PicTar-5 way and the experimental one, TarBase. In this study, for the first time, the RNAhybrid database sets were introduced in a computational program.


Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.

Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S - BMC Bioinformatics (2009)

JTarget main menu. (A) Jtarget interface (B) The target genes of miR-21 as listed by the procedure "Compare All'' (4 databases).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697644&req=5

Figure 1: JTarget main menu. (A) Jtarget interface (B) The target genes of miR-21 as listed by the procedure "Compare All'' (4 databases).
Mentions: JTarget main goal is to find the target genes of a given miRNA derived from 1 to 6 databases and compare any possible combination of the results from these databases. The available databases are TargetScan, miRanda, RNAhybrid, PicTar-4 way, PicTar-5 way and TarBase. Following the insertion of a specific miRNA name, 3 possible scenarios are given. The user can obtain the resulting target genes from: a) one database only, b) two or more databases or c) all combined databases. JTarget contains text fields, buttons and one central text area for the interaction with the user (Figure 1A). To find the target genes of a miRNA from a single database, the "Search by miRNA" option has to be selected and a miRNA name (e.g. miR-21) should be given. Then, a database (e.g. TargetScan) should be marked and the results are presented in the central text area by clicking the "Find Targets" button. The common results from 2 or more databases can be obtained by marking the desirable databases and clicking the "Compare database results" button. The available databases are: TargetScan, miRanda, RNAhybrid, PicTar-4 way, PicTar-5 way and the experimental one, TarBase. In this study, for the first time, the RNAhybrid database sets were introduced in a computational program.

Bottom Line: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation.GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering.GOmir can freely be downloaded BRFAA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cell & Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece. mroubelaki@bioacademy.gr

ABSTRACT

Background: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation. Predicting or verifying mRNA targets of specific miRNAs is a difficult process of great importance.

Results: GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application.

Conclusion: GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering. Additionally, a reverse search initiated by a potential target can also be conducted. GOmir can freely be downloaded BRFAA.

Show MeSH